dChip Software: Analysis and visualization of gene expression and SNP microarrays


 Manual PDF: 2005, 2002

(old site)




 User Group


  User Help

dChip was started in Wing Wong Lab and is developed and maintained by Cheng Li Lab. The current support is NIH grant R01 GM077122.

Table of Contents

Data processing

Introduction, download, and user support                         

Prepare data, file format and example method description

Gene information file, make or classify gene list

Read in CEL and CDF files, sample information file

Read external data file                                                           

Combine data from different array types or species 

Automated analysis                                                   

Interface with R software

Designing experiments                                                                                                 


Probe-level analysis

Normalize arrays                                                                    

View array image, export image and CEL file

View and export PM/MM probe data                                     

Compute and export model-based expression value, outlier array

Exon and tiling array analysis


High-level analysis

Array list file, handle batch effect

Filter genes

Compare samples                                                                   

Hierarchical clustering                                                                                

Gene function enrichment analysis                                        

Analysis of Variance and correlation filtering

Map genes to chromosome                                                     

Classify samples by linear discriminant analysis

Principal component analysis


SNP array analysis

SNP array data processing

View expression, SNP, CGH data along chromosome

LOH and copy number analysis                                             

Chromosome regions, clustering using SNP data

Parametric linkage analysis                                                    

Allele sharing analysis                                                                                   

Compute and permute summary score



References and acknowledgments

Li 03.pdf
Cheng Li,
Nov 6, 2012, 8:28 AM
Cheng Li,
Nov 6, 2012, 8:28 AM